User: giulia.pasquesi

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Posts by giulia.pasquesi

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Comment: C: rlog, lfcShrink and vst on gene subset
... Thank you so much for the clarification.  It is exactly what I was looking for!   ...
written 9 weeks ago by giulia.pasquesi0
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Comment: C: rlog, lfcShrink and vst on gene subset
... I did't know about the [idx] flag but isn't it gonna specify the samples I want to include? I would like to plot the variances for only a subset of genes (therefore by rows and not by column in a matrix. Provided the normalization was based on all genes, otherwise the library size would be incorrect ...
written 9 weeks ago by giulia.pasquesi0
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rlog, lfcShrink and vst on gene subset
... I am analyzing a dataset that includes both gene and transposable element raw counts.  I am only interested in analyzing the differential expression of TEs, but still need to create and normalize the entire dataset. For the DE analysis itself it is not a major problem, because I can retrieve the res ...
deseq2 plot subsetting written 10 weeks ago by giulia.pasquesi0 • updated 9 weeks ago by Michael Love19k
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DESeq, DESeq2 or EdgeR normalization for gene expression on multiple tissues without replicates ?
... Hello all, I know this is probably a very old (and sadly still ongoing) topic, but I would like your advice anyway. I have RNAseq data processed in TETranscript for 7 different Zebrafish tissues (testis, ovary, heart, kidney ...). I am not strictly interested in DE analyses (at least not yet), as I ...
normalization edger deseq2 written 5 months ago by giulia.pasquesi0 • updated 5 months ago by Aaron Lun20k

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